Article
Ecology
Xiao Wang, Quanli Xu, Jing Liu
Summary: A new method based on geographic similarity is proposed for obtaining pseudo-absence data. The results show that this method can improve model accuracy and provide valuable insights into improving invasive plant distribution predictions.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Cleber Ten Caten, Tad Dallas
Summary: Spatial and environmental thinning of occurrence data usually fails to improve the performance of species distribution models (SDMs), and may even lead to a decrease in model performance.
Article
Environmental Sciences
Yuyang Xian, Yongquan Lu, Guilin Liu
Summary: Global climate change caused by fossil energy consumption threatens the habitat of pangolins. MaxEnt modeling reveals that temperature, precipitation, geomorphology, and vegetation coverage affect the habitats of different pangolin species. Human activities pose a threat to pangolin habitats, but labor transfer in southern China mitigates the negative impact in rural areas. Illegal pangolin trade is a significant threat, and future scenarios show changes in habitat for different pangolin species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biodiversity Conservation
Leonardo de Sousa Miranda, Marcelo Awade, Rodolfo Jaffe, Wilian Franca Costa, Leonardo Carreira Trevelin, Rafael Cabral Borges, Rafael Melo de Brito, Leandro Reverberi Tambosi, Tereza Cristina Giannini
Summary: The study aimed to enhance the connectivity of protected areas in the eastern Amazon to ensure the conservation of forest species, considering the joint effects of habitat fragmentation and climate change. By analyzing species movement flow and habitat suitability models, the study identified potential corridors for species movement, with differences in direction and forest cover based on the different approaches used. The results highlight the importance of methodological redundancy and efficient strategies for prioritizing areas for connectivity to address biodiversity threats and protect species in a rapidly changing world.
BIOLOGICAL CONSERVATION
(2021)
Article
Environmental Sciences
Asad Ali, Farrah Zaidi, Syeda Hira Fatima, Said Munir
Summary: The study utilized binomial kriging to model the spatial distribution of three species of flies in livestock in Khyber Pakhtunkhwa, Pakistan, showing a good fit of the spatial models. It was found that land-use-land-cover was a significant factor affecting the spatial distribution of all three species, while elevation acted as a barrier for the invading species, Wohlfahrtia magnifica, limiting its distribution potential.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2021)
Article
Fisheries
Iosu Paradinas, Janine B. Illian, Alexandre Alonso-Fernaendez, Maria Grazia Pennino, Sophie Smout
Summary: Species Distribution Models (SDMs) play a crucial role in fisheries management, and the integration of various data sources has become an attractive approach to improve model predictions. Integrated Species Distribution Models (ISDMs) have the ability to formally combine different types of data and account for scale proportional gear efficiencies. This study demonstrates the use of ISDMs to integrate information from afishery-independent trawl survey and a fishery-dependent trammel net observations, showing the sensitivity of model outputs to different weightings for the commercial data. The results are compared to ensemble modelling, highlighting the requirement for consistency in response variables and link functions across models.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Review
Multidisciplinary Sciences
Mariano J. Feldman, Louis Imbeau, Philippe Marchand, Marc J. Mazerolle, Marcel Darveau, Nicole J. Fenton
Summary: Citizen science (CS) has gained popularity in the past two decades, providing a low-cost approach for scientists to collect species occurrence information at large spatial scales. However, disparities in taxonomic and geographic coverage remain in studies using CS as a data source for species distribution models. While the number of papers using CS for SDMs has increased rapidly, especially in Western Europe and North America, there is still a lack of research on certain taxa and regions.
Review
Ecology
Heather L. Kopsco, Rebecca L. Smith, Samniqueka J. Halsey
Summary: Species distribution models are useful tools for predicting tick habitat suitability and range movement, but there is a need for standardized protocols for tick vector species distribution and ecological niche modeling.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Malcolm O'Toole, Nuno Queiroz, Nicolas E. Humphries, David W. Sims, Ana M. M. Sequeira
Summary: Telemetry datasets are increasingly large and cover a wide range of species, allowing for the understanding of species' spatial use. However, biases in tracking datasets can affect model performance, with tagging location and track length having the greatest impact. Adding less biased tracks can help overcome these biases.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Marine & Freshwater Biology
Anais Charbonnel, Patrick Lambert, Geraldine Lassalle, Eric Quinton, Antoine Guisan, Lise Mas, Guillaume Paquignon, Marie Lecomte, Marie-Laure Acolas
Summary: This study investigates the distribution of the critically endangered European sturgeon (Acipenser sturio) and identifies key factors influencing its habitat selection. The results suggest that bathymetry, temperature, salinity, bottom current velocity, and distance to the source population are important predictors of A. sturio distribution, while substrate type has little influence. The most suitable marine areas for A. sturio are predicted to be along the French Atlantic coast, the Seine and Somme bays, the Rhine delta, and certain coastal areas in the Cantabrian Sea.
ESTUARINE COASTAL AND SHELF SCIENCE
(2023)
Article
Biodiversity Conservation
Abeje Kassie Teme, Afework Bekele Simegn, Bezawork Afework Bogale
Summary: The present study investigated the species composition, diversity, distribution, and richness of endemic frog species in the Keffa area of southwest Ethiopia. The study found that agricultural land and riverine forest had a higher number of endemic frog species, highlighting the importance of their conservation. The Keffa area is a significant habitat for endemic frog species in Ethiopia, emphasizing the need for conservation efforts.
GLOBAL ECOLOGY AND CONSERVATION
(2022)
Article
Zoology
Shawn D. Snyder, William B. Sutton, David A. Steen
Summary: Habitat management and species conservation plans are crucial for protecting biodiversity. This study focused on the Pygmy Rattlesnake and used a species distribution model to identify suitable habitat primarily in riparian areas. The findings provided valuable insights for conservation efforts.
Article
Ecology
Dallas R. R. Levey, Michael A. A. Patten, Alejandro Estrada
Summary: Long-term land-use change has significant impacts on tropical bird communities, leading to habitat loss, degradation, and fragmentation, resulting in challenges for land management and conservation. The study developed a novel Bayesian species occupancy framework to evaluate bird community changes in Palenque, Chiapas, Mexico. The results showed that open area species had higher population increases than forest specialists over time, and functional traits such as habitat types, body mass, and dietary breadth were associated with bird population trends. Conservation of primary forests and protection of rare natural savanna patches are crucial for the preservation of habitat and dietary specialists and prevention of further extirpation of native species.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Engineering, Marine
Sheng-Yuan Teng, Nan-Jay Su, Ming-An Lee, Kuo-Wei Lan, Yi Chang, Jinn-Shing Weng, Yi-Chen Wang, Riah Irawati Sihombing, Ali Haghi Vayghan
Summary: The study constructed a spatial habitat distribution of black sea bream using data from 2015 to 2018 and found that the species concentrated in coastal waters, showing synchronous trends with seasonal dynamics of the marine environment. Chlorophyll-a concentration and bathymetry were identified as significant factors influencing black sea bream's habitat selection.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2021)
Article
Environmental Sciences
Goncalo Duarte, Paulo Branco, Gertrud Haidvogl, Maria Teresa Ferreira, Didier Pont, Pedro Segurado
Summary: This study aims to establish a new methodological framework (iPODfish) to obtain a more complete representation of the historical occurrences of diadromous fish species across their full distribution range. The method is based on assumptions derived from freshwater network features, fish ecology, and known historical occurrences, and utilizes a tree-like decision process to establish historical pseudo-occurrences at the segment scale. Despite its inference nature, iPODfish is a conservative procedure that can be applied to any diadromous fish species with a relevant amount of historical data available, providing reliable historical occurrence outputs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Ecology
Anna Norberg, Nerea Abrego, F. Guillaume Blanchet, Frederick R. Adler, Barbara J. Anderson, Jani Anttila, Miguel B. Araujo, Tad Dallas, David Dunson, Jane Elith, Scott D. Foster, Richard Fox, Janet Franklin, William Godsoe, Antoine Guisan, Bob O'Hara, Nicole A. Hill, Robert D. Holt, Francis K. C. Hui, Magne Husby, John Atle Kalas, Aleksi Lehikoinen, Miska Luoto, Heidi K. Mod, Graeme Newell, Ian Renner, Tomas Roslin, Janne Soininen, Wilfried Thuiller, Jarno Vanhatalo, David Warton, Matt White, Niklaus E. Zimmermann, Dominique Gravel, Otso Ovaskainen
ECOLOGICAL MONOGRAPHS
(2019)
Article
Ecology
Jenni Niku, Francis K. C. Hui, Sara Taskinen, David I. Warton
METHODS IN ECOLOGY AND EVOLUTION
(2019)
Article
Ecology
Alexander T. Sentinella, David I. Warton, William B. Sherwin, Catherine A. Offord, Angela T. Moles
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2020)
Article
Environmental Sciences
Kingsley J. Griffin, Luke H. Hedge, David Warton, Karen L. Astles, Emma L. Johnston
Summary: Urbanised estuaries, ports, and harbours are now being considered by coastal spatial management initiatives due to their high biodiversity and value to local residents. Assessments of recreational activities in these areas can help avoid conflicts, but existing models need to be developed at a scale relevant to regulatory bodies.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Mathematical & Computational Biology
Firouzeh Noghrehchi, Jakub Stoklosa, Spiridon Penev, David I. Warton
Summary: This article demonstrates the equivalence between multiple imputation and stochastic expectation-maximization approximation to likelihood, and proposes using likelihood-based model selection tools to choose the best imputation model. Selecting an appropriate imputation model is crucial to minimizing bias in inference, and the BIC method shows promise in selecting the correct imputation model.
STATISTICS IN MEDICINE
(2021)
Article
Environmental Sciences
Jenni Niku, Francis K. C. Hui, Sara Taskinen, David Warton
Summary: The study focuses on analyzing the interaction between environmental variables and species trait variables in ecological community studies, specifically utilizing the fourth-corner model to account for these interactions. A proposed fourth-corner latent variable model is introduced to better capture the correlation between species, environment-trait interactions, and species-specific random slopes. Simulation results indicate that the proposed model performs well in testing for interaction coefficients, showing a lower risk of inflated Type I error compared to other available models.
Article
Ecology
Gordana C. Popovic, Francis K. C. Hui, David Warton
Summary: Data visualization is crucial in data analysis, especially in ecology where challenges arise from numerous variables and non-normal distributions. Ordination is a common and powerful approach to simplify plotting by reducing multiple response variables to a few. Model-based unconstrained ordination methods have gained popularity in recent years, particularly for estimating latent ecological gradients.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Statistics & Probability
David I. Warton
Summary: This article proposes a method of constructing global envelopes on residual plots to validate regression model assumptions and study their properties through simulation experiments. The global envelope tests perform better than commonly used tests at detecting violations of distributional and linearity assumptions.
AMERICAN STATISTICIAN
(2023)
Article
Biochemistry & Molecular Biology
Mingjie Luo, Yinqiu Ji, David Warton, Douglas W. Yu
Summary: Accurately extracting species-abundance information from DNA-based data is important for various applications. This study focuses on distinguishing within-sample across-species quantification and across-sample within-species quantification. The authors review literature on methods to remove biases and noise in DNA-based data sets and propose using DNA spike-ins as well as a model-based estimator to correct for pipeline noise.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Han Wang, Colin Prentice, Ian J. Wright, David I. Warton, Shengchao Qiao, Xiangtao Xu, Jian Zhou, Kihachiro Kikuzawa, Nils Chr. Stenseth
Summary: The life span of leaves is positively correlated with their mass per unit area (LMA), but the underlying mechanism remains unclear. By analyzing large leaf trait datasets, we found that this empirical generalization is a result of natural selection, which maximizes average net carbon gain over the leaf life cycle. We demonstrated how evergreen and deciduous species with different construction costs (assumed proportional to LMA) are selected by light, temperature, and growing-season length in predictable ways. Moreover, we explained the observed divergent latitudinal trends in evergreen and deciduous LMA and showed how local distributions of LMA arise from selection under different environmental conditions acting on the species pool. These findings highlight how optimality principles can contribute to a new theory for plant geography and terrestrial carbon dynamics.
Article
Statistics & Probability
Elliot Dovers, Wesley Brooks, Gordana C. C. Popovic, David I. I. Warton
Summary: Log-Gaussian Cox processes (LGCPs) provide a framework for regression-style modeling of point patterns with spatial latent effects. We propose a novel methodology for fitting LGCP models that addresses the challenges of marginal likelihood and high dimensional integral. The method combines variational approximation, reduced rank interpolation, automatic differentiation, and integral approximation using the Laplace method. Simulation and real data application show promising results in terms of computational speed and accuracy compared to existing approaches.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2023)
Article
Ecology
Ben Maslen, Gordana Popovic, Michelle Lim, Ezequiel Marzinelli, David Warton
Summary: Sample size estimation through power analysis is crucial in ecological studies. A proposed power analysis procedure addresses challenges in multivariate abundance data collection by using a Gaussian copula model, assuming a common effect size across all taxa, and using a critical value approach to estimate power. This procedure was demonstrated on fish assemblage data and is available in the ecopower R software package.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Correction
Ecology
A. T. Sentinella, D. Warton, W. B. Sherwin, C. A. Offord, A. T. Moles
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Statistics & Probability
Ian W. Renner, David I. Warton, Francis K. C. Hui
Summary: Point process models are natural for modeling data as point events, particularly for Poisson counts and regression. However, traditional criteria like BIC cannot be used for model selection in this context, requiring a redefinition of evaluation metrics. This study develops conditions for penalized likelihood fitting of point process models based on asymptotic results, and discusses the challenges of extending these results to the broader class of Gibbs models.
AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Robert Nguyen, James Day, David Warton, Oscar Lane
